A user-friendly program written in Python 3 (Comput. Phys. Commun., 2020, 256, 107457). It was designed to use direct-dynamics to calculate thermal rate constants of chemical reactions and to simulate chemical kinetics mechanisms. It was designed together with Donald G. Truhlar from the University of Minnesota (http://truhlar.chem.umn.edu).
For reaction processes with many elementary steps, each of these steps can be calculated using conventional transition state theory (TST) or In this version, Pilgrim can calculate thermal rate constants with the canonical version of the variational transition state theory (CVT), which requires the calculation of the minimum energy path (MEP) associated to each elementary step. Moreover, multi-dimensional quantum effects can be incorporated through the small-curvature tunneling approximation (SCT). The above methodologies are available for reactions involving a single structure and for reactions involving flexible molecules with multiple conformations. Specifically, for systems with many conformers the program can evaluate each of the elementary reactions by multi-path canonical variational transition state theory (MP-CVT) or multi-structural VTST (MS-VTST). Torsional anharmonicity can be also incorporated through the Torsiflex, MSTor or Q2DTor programs.
Once all the rate constants of the chemical processes of interest are known, by means of their calculation using Pilgrim or by using an analytical expression, it is possible to simulate the whole process using kinetic Monte Carlo (KMC). This algorithm allows performing a kinetics simulation and monitoring the evolution of each chemical species with time, as well as providing its chemical yield.
Department of Physical Chemistry Faculty of Chemistry University of Santiago de Compostela Spain
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